R/plotDMRs.R

In dmrseq: Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

#' Plot Differentially Methylated Regions
#'
#' Generates trace plots of methylation proportions by genomic position.
#' 
#' Creates aesthetially pleasing DMR plots. By default will plot individual
#' points with size proportional to coverage, along with a smoothed line 
#' for each sample. Elements will be colored by biological condition 
#' (\code{label}). Also has functionality to add annotations below the main
#' plot (CpG category, genes) if \code{annoTrack} is specified.
#' 
#' @param BSseq An object of class BSseq.
#' 
#' @param regions A data.frame containing the DMRs (output from the main
#' \code{dmrseq}) function.
#' 
#' @param extend Describes how much the plotting region should be extended in
#'  either direction. The total width of the plot is equal to the width of the 
#'  region plus twice extend.
#' 
#' @param main The plot title. The default is to construct a title with 
#' information about which genomic region is being plotted.
#' 
#' @param addRegions A set of additional regions to be highlighted on the 
#' plots. Same format as the \code{regions} argument.
#' 
#' @param annoTrack a \code{GRangesList} object with two elements returned
#' by \code{\link{getAnnot}}. The first
#' contains CpG category information in the first element (optional)
#' coding gene sequence information in the second element (optional).
#' At least one of these elements needs to be non-null in order for 
#' any annotation to be plotted, but it is not necessary to contain
#' both.
#' 
#' @param col The color of the methylation estimates. It is recommended to 
#' leave this value as default (NULL), and specify a value of 
#' \code{testCovariate} to indicate which column of \code{pData(bs)}
#' to use as a factor for coloring the points and lines of the plot.
#' Alternatively, you can specify particular colors by 
#' passing this information through the \code{pData} slot of the
#' object \code{BSseq} (a \code{data.frame} that houses metadata). To do 
#' so, place the color value for each sample in a column titled \code{col}, 
#' and leave this argument as its default value of NULL. Alternatively,
#' you may specify a vector of color values (one for each sample), but 
#' you *must* make sure that this vector is in the same order as the samples
#' are in the BSseq object. If NULL and no \code{col} column is found in 
#' \code{pData}, then estimates are plotted in black for all samples.
#' 
#' @param lty The line type of the methylation estimates. It is recommended to
#' pass this information through the \code{pData} slot of the
#' object \code{BSseq} (a \code{data.frame} that houses metadata). To do 
#' so, place the line type value for each sample in a column titled \code{lty}, 
#' and leave this argument as its default value of NULL. Alternatively,
#' you may specify a vector of line type values (one for each sample), but 
#' you *must* make sure that this vector is in the same order as the samples
#' are in the BSseq object. If NULL and no \code{lty} column is found in 
#' \code{pData}, then estimates are plotted with \code{lty=1} for all samples.
#' 
#' @param lwd The line width of the methylation estimates. It is recommended to
#' pass this information through the \code{pData} slot of the
#' object \code{BSseq} (a \code{data.frame} that houses metadata). To do 
#' so, place the line width value for each sample in a column titled \code{lwd},
#' and leave this argument as its default value of NULL. Alternatively,
#' you may specify a vector of line width values (one for each sample), but 
#' you *must* make sure that this vector is in the same order as the samples
#' are in the BSseq object. If NULL and no \code{lwd} column is found in 
#' \code{pData}, then estimates are plotted with \code{lwd=1} for all samples.
#' 
#' @param label The condition/population labels for the plot legend. If NULL
#' (default) this is taken from the \code{testCovariate} column of 
#' \code{pData}. Alternatively, you can pass in labels by 
#' adding this information through the \code{pData} slot of the
#' object \code{BSseq} (a \code{data.frame} that houses metadata). To do 
#' so, place the labels for each sample in a column titled \code{label}, 
#' and leave this argument as its default value of NULL.
#' You may instead specify an arbitrary vector of labels (one for each sample),
#' but be aware that you *must* make sure that this vector is in the same order 
#' as the samples are in the BSseq object. If NULL, and \code{testCovariate} is
#' also NULL and no \code{label} column is found in 
#' \code{pData}, then no legend is created.
#' 
#' @param mainWithWidth logical value indicating whether the default title
#' should include information about width of the plot region.
#' 
#' @param regionCol The color used for highlighting the region.
#' 
#' @param addTicks logical value indicating whether tick marks showing the
#'  location of methylation loci should be added. Default is TRUE.
#' 
#' @param addPoints logical value indicating whether the individual 
#' methylation estimates be plotted as points.
#' 
#' @param pointsMinCov The minimum coverage a methylation loci need in 
#' order for the raw methylation estimates to be plotted. Useful for filtering
#' out low coverage loci. Only used if addPoints = TRUE. Default value is 1 
#' (no filtering).
#' 
#' @param highlightMain logical value indicating whether the plot region 
#' should be highlighted.
#' 
#' @param stat logical value indicating whether the region statistic 
#' should be displayed in the plot title. The value is extracted from the
#' \code{regions} argument.
#' 
#' @param qval logical value indicating whether the region FDR estimate  
#' (q-value) should be displayed in the plot title. The value is extracted 
#' from the \code{regions} argument.
#' 
#' @param verbose logical value indicating whether progress messages 
#' should be printed to the screen.
#' 
#' @param testCovariate integer value or vector indicating which of columns of
#'  \code{pData(bs)} contains the covariate of interest. 
#'  This is used to construct the sample labels and colors (unless this is
#'  over-ridden by specifying \code{label}).
#'  
#' @param includeYlab a logical indicating whether to include the Y axis
#'  label 'Methylation' (useful to turn off if combining multiple region
#'  figures and you do not want to include redundant y axis label information)
#'  
#' @param compareTrack a named GenomicRangesList item that contains up to four
#' custom tracks (GenomicRanges objects) which will be plotted below the region.
#' Only one of `compareTrack` or `annoTrack` can be specified since there is
#' only for plotting either the built in GpG category and exon tracks, *or* a
#' custom set of tracks.
#' 
#' @param labelCols a character vector with names of the mcols slot of the 
#' GenomicRanges items in `compareTrack'. Only used if plotting custom
#' tracks using the `compareTrack' argument. If specified, the (first) value
#' in that column is printed along with a label that includes the name of the
#' list item. If NULL (default), just the name of the track is printed.
#' 
#' @param horizLegend logical indicating whether the legend should be 
#' horizontal instead of vertical (default FALSE). This is useful if you need
#' to plot many labels and want to preserve whitespace.
#' 
#' @param addLines logical indicating whether to plot smooth lines between 
#' points. Default is true. Can be useful to turn this off for very small 
#' regions.
#' 
#' @export
#' 
#' @return None (generates a plot)
#' 
#' @importFrom RColorBrewer brewer.pal
#' @importFrom grDevices hcl rainbow
#' @importFrom graphics arrows
#' 
#' @examples
#' 
#' # load the example data
#' data(BS.chr21)
#' 
#' # load example results (computed with dmrseq function)
#' data(dmrs.ex)
#' 
#' # get annotation information (using getAnnot function)
#' # here we'll load the example annotation from chr21
#' data(annot.chr21)
#' 
#' # plot the 1st DMR
#' plotDMRs(BS.chr21, regions=dmrs.ex[1,], testCovariate=1,
#'    annoTrack=annot.chr21)
#' 
plotDMRs <- function(BSseq, regions = NULL, testCovariate = NULL, 
    extend = (end(regions) - start(regions) + 1)/2, main = "", 
    addRegions = regions, annoTrack = NULL, col = NULL, 
    lty = NULL, lwd = NULL, label = NULL, mainWithWidth = TRUE, 
    regionCol = .alpha("#C77CFF", 
        0.2), addTicks = TRUE, addPoints = TRUE, pointsMinCov = 1, 
    highlightMain = FALSE, 
    qval = TRUE, stat = TRUE, verbose = TRUE, includeYlab = TRUE, 
    compareTrack = NULL, 
    labelCols = NULL, horizLegend = FALSE,
    addLines = TRUE) {
    # adapted from plotManyRegions from bsseq plot to take 
    # in a vector of qval values
    # (1 per region in regions argument) to be displayed in
    # the plot title.  set
    # addPoints = TRUE to plot individual points sized by coverage
    # and one smooth
    # (loess) line per sample instead of a uniform-sized verbatim 
    # line going through
    # each observation
    if (!addLines && !addPoints)
      stop("At least one of addLines or addPoints must be true")
    if (verbose) 
        message("[plotDMRs] Plotting ", nrow(regions), " DMRs")
    if (!is.null(regions)) {
        if (is(regions, "data.frame")){
            gr <- data.frame2GRanges(regions, keepColumns = FALSE)
        }else{ 
          gr <- regions
        }
        if (!is(gr, "GRanges")) 
            stop("'regions' needs to be either a 'data.frame' ",
                        " or a 'GRanges' ")
    } else {
        gr <- granges(BSseq)
    }
    gr <- resize(gr, width = 2 * extend + width(gr), fix = "center")
    BSseq <- subsetByOverlaps(BSseq, gr)
    
    if (!is.null(annoTrack) && !is.null(compareTrack)) 
        stop("Choose either annoTrack or compareTrack; can't plot both")
    
    if (length(start(BSseq)) == 0) 
        stop("No overlap between BSseq data and regions")
    if (!is.null(main) && length(main) != length(gr)) 
        main <- rep(main, length = length(gr))
    
    if (length(extend) == 1) {
        extend <- rep(extend, length(gr))
    }
    
    if (!is.null(testCovariate)) {
      coeff <- seq(2, (1 + length(testCovariate)))
      testCov <- as.character(pData(BSseq)[, testCovariate])
      if (length(unique(testCov)) > 2 && !is.numeric(testCov) && length(coeff) == 1)
        coeff <- seq(coeff, coeff + length(unique(as.character(testCov))) - 2 )
      
      design <- model.matrix(~testCov)
        
        if (is.null(col) && !("col" %in% names(pData(BSseq)))) {
            cov.unique <- unique(design[, coeff, drop = FALSE])
            ncol <- nrow(cov.unique) 
            
            colors <- gg_color_hue(ncol)
            if (ncol == 2) {
                colors <- c("mediumblue", "deeppink1")
            }
            colors <- cbind(cov.unique, 
                            colors[rank(as.numeric(rowSums(cov.unique)), 
                                        ties.method = "first")])
            colmat <- colors[, -ncol(colors), drop = FALSE]
            colmat <- apply(colmat, 2, as.numeric)
            z <- colors[,ncol(colors)][
                         match(data.frame(t(design[, coeff, drop = FALSE])), 
                               data.frame(t(colmat)))]
            
            pData(BSseq)$col <- as.character(z)
        }
        
        if (is.null(label)  && !("label" %in% names(pData(BSseq))))  {
            pData(BSseq)$label <- paste0(pData(BSseq)[, testCovariate])
        }
    }
    
    if (!is.null(label) || "label" %in% names(pData(BSseq))) {
        if(!is.null(label)){
          labs <- label
        }else{
          labs <- pData(BSseq)[["label"]]
        }
        if(horizLegend){
          wiggle <- max(nchar(labs)) * 0.4
        }else{
          wiggle <- length(unique(labs)) * 0.9
        }
        opar <- par(mar = c(0, 4.1, 0, wiggle), 
                    oma = c(0, 0, 2.5, 1))
    } else {
        opar <- par(mar = c(0, 4.1, 0, 0), oma = c(0, 0, 2.5, 1))
    }
    on.exit(par(opar))
    
    for (ii in seq(along = gr)) {
        if (verbose && ii%%100 == 0) {
            cat(sprintf("..... Plotting region %d (out of %d)\n", ii, 
                        nrow(regions)))
        }
        
        .plotSingleDMR(BSseq = BSseq, region = regions[ii, ], 
            extend = extend[ii], main = main[ii], col = col, lty = lty, 
            lwd = lwd, label = label, addRegions = addRegions, 
            regionCol = regionCol, mainWithWidth = mainWithWidth, 
            annoTrack = annoTrack, addTicks = addTicks, addPoints = addPoints, 
            pointsMinCov = pointsMinCov, highlightMain = highlightMain, 
            qval = qval, stat = stat, includeYlab = includeYlab, 
            compareTrack = compareTrack, labelCols = labelCols,
            horizLegend = horizLegend, addLines = addLines)
    }
}